According to shallow water, vast area, sailing inconvenience, the crest of Dongsha Atoll have less complete survey for a long time. However, the investigation is not conducive to the traditional surveys, but just very suitable for satellite images of large area investigation. This study used multispectral optical satellite images cooperated with in situ ground truth data, to investigate bottom and habitat's distribution of the atoll crest. By classification by satellite images, the crest could be classified into 4 habitats: sea grass, live coral, sand and rock, beside the habitats distribution and the area also been estimated. Overall, the sea grass habitat distributed inside of the crest, the rock habitat mostly distributed outside of the crest and the live coral habitat located in between the two. The accuracy evaluation of the habitats survey also has been completed by ground truth and the correct rate could obtain around 85%. In addition, this study also used the satellite images in different seasons, the sea grass in the summer there is a more bushy growth trend, while the growth of algae in the autumn there are relatively strong trend.